diff --git a/common.py b/common.py index 8c1a723..8669dfa 100644 --- a/common.py +++ b/common.py @@ -1,3 +1,3 @@ # The path to the freezeman sample submission template used by the convertor. -FMS_SUBMISSION_TEMPLATE_PATH = "config/fms_sample_submission_template_4.9.xlsx" +FMS_SUBMISSION_TEMPLATE_PATH = "config/fms_sample_submission_template_4.12.xlsx" diff --git a/config/fms_sample_submission_template_4.12.xlsx b/config/fms_sample_submission_template_4.12.xlsx new file mode 100644 index 0000000..84bf426 Binary files /dev/null and b/config/fms_sample_submission_template_4.12.xlsx differ diff --git a/convertor/freezeman/freezeman_config_data.py b/convertor/freezeman/freezeman_config_data.py index 013b8fd..51508cc 100644 --- a/convertor/freezeman/freezeman_config_data.py +++ b/convertor/freezeman/freezeman_config_data.py @@ -7,7 +7,7 @@ "PROJECT": "Project", "COHORT": "Cohort", "EXPERIMENTAL_GROUP": "Experimental Group", - "TAXON": "NCBI Taxon ID #", + "TAXON": "Taxon", "SAMPLE_COORD": "Sample Coord", "CONTAINER_KIND": "Container Kind", "CONTAINER_NAME": "Container Name", @@ -17,9 +17,6 @@ "INDIVIDUAL_NAME": "Individual Name", "INDIVIDUAL_ALIAS": "Individual Alias", "SEX": "Sex", - "PEDIGREE": "Pedigree", - "MOTHER_NAME": "Mother Name", - "FATHER_NAME": "Father Name", "VOLUME": "Volume (uL)", "CONCENTRATION": "Conc. (ng/uL)", "COLLECTION_SITE": "Collection Site", diff --git a/convertor/freezeman/sample.py b/convertor/freezeman/sample.py index 37121ee..9b17ce7 100644 --- a/convertor/freezeman/sample.py +++ b/convertor/freezeman/sample.py @@ -14,9 +14,6 @@ def __init__(self): self.containerCoord = "" self.individualName = "" self.sex = "" - self.pedigree = "" - self.motherName = "" - self.fatherName = "" self.volume = "" self.concentration = "" self.collectionSite = "" diff --git a/convertor/freezeman/sample_headers.py b/convertor/freezeman/sample_headers.py index 4c5d6cf..19e10e6 100644 --- a/convertor/freezeman/sample_headers.py +++ b/convertor/freezeman/sample_headers.py @@ -13,9 +13,6 @@ class SampleHeaders: CONTAINER_COORD = "Container Coord" INDIVIDUAL_NAME = "Individual Name" SEX = "Sex" - PEDIGREE = "Pedigree" - MOTHER_NAME = "Mother Name" - FATHER_NAME = "Father Name" VOLUME = "Volume (uL)" CONCENTRATION = "Conc. (ng/uL)" COLLECTION_SITE = "Collection Site" @@ -39,9 +36,6 @@ class SampleHeaders: CONTAINER_COORD, INDIVIDUAL_NAME, SEX, - PEDIGREE, - MOTHER_NAME, - FATHER_NAME, VOLUME, CONCENTRATION, COLLECTION_SITE, diff --git a/convertor/moh/moh_config_data.py b/convertor/moh/moh_config_data.py index 9fb94ab..fa89063 100644 --- a/convertor/moh/moh_config_data.py +++ b/convertor/moh/moh_config_data.py @@ -74,9 +74,9 @@ "TUBE": "Tube" }, "taxonTypeMap": { - "Eukaryota:Homo sapiens (Taxon ID:9606)": 9606, - "Eukaryota:Mus musculus (Taxon ID:10090)": 10090, - "Viruses:Severe acute respiratory syndrome coronavirus 2 (Taxon ID:2697049)": 2697049, + "Eukaryota:Homo sapiens (Taxon ID:9606)": "Homo sapiens", + "Eukaryota:Mus musculus (Taxon ID:10090)": "Mus musculus", + "Viruses:Severe acute respiratory syndrome coronavirus 2 (Taxon ID:2697049)": "Sars-Cov-2", "NOT_IN_MOH": "Ixodes Scapularis" }, "concentration_units": { diff --git a/version.py b/version.py index fdbf481..ae971e6 100644 --- a/version.py +++ b/version.py @@ -1,4 +1,4 @@ -CONVERTOR_VERSION = '4.9' +CONVERTOR_VERSION = '4.12' # 3.12.1: Updated streamlit and Pillow because of security warnings # 3.13.0: Updated for freezeman 3.13.0 submission template @@ -11,4 +11,5 @@ # 4.4: Updated version number only - no template changes # 4.5: Updated version number - Template replaced individuals ID by Name # 4.6: Updated version number - no template changes -# 4.9: Updated version number - no template changes \ No newline at end of file +# 4.9: Updated version number - no template changes +# 4.12: Updated version number - Template removed header fields and changed Taxon ID to Taxon name